MaizeGDB Phylostrata Tool: Exploring evolutionary origins of maize proteins
Laura E Tibbs-Cortes, Oliva C Haley, John L Portwood, Ethalinda K Cannon, Margaret R Woodhouse, Carson M AndorfAbstract
Motivation
Phylostratigraphic analysis identifies the evolutionary origins and level of conservation of proteins, facilitating research in evolutionary biology and comparative genomics.
Results
We developed the MaizeGDB Phylostrata Tool, a custom web application that enables users to explore the evolutionary origins of proteins in maize (Zea mays), a globally important crop and model organism. This tool features interactive visualizations and detailed gene pages incorporating subcellular localization, Gene Ontology (GO) terms, and links to resources for homologs, facilitating comparison of gene functions across evolutionary time. The tool also provides download links for full-proteome phylostratigraphic results for 26 maize inbreds (B73 and the NAM founders). From these, we identified genome- and subgenome-wide trends, finding that more conserved proteins tended to be longer and more highly expressed. Finally, we provide code including updates to the `phylostratr` R package to make it more robust to taxonomic updates, as well as example scripts for phylostratigraphic analysis and webtool development for the use of researchers and curators of other species.
Availability and implementation
The MaizeGDB Phylostrata Tool is freely available at https://phylostrata.maizegdb.org. Scripts used for the analysis and web tool are available at https://github.com/LTibbs/PhylostrataWebtool.